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Home » DataWarrior » Functionality » Row wise chemical reaction (Wish to combine Carboxylic acids in one column with AA in another, not combinatorially)
Row wise chemical reaction [message #718] Fri, 06 December 2019 19:54 Go to next message
P_Fitz
Messages: 14
Registered: November 2019
Junior Member
The enumerate chemical libraries feature of data warrior is awesome, but does not do quite what I want it to for this particular application.

I have a list of Carboxylic acids that correspond with specific Amino acids that they are combined with. Enumerate chemical libraries with these sets creates all possible combinations of the two. Is there a way to just combine specific Amino acids with specific Carboxylic acids? Basically I just want to combine reactants row-wise rather than combinatorially.

Thanks!

Patrick
Re: Row wise chemical reaction [message #724 is a reply to message #718] Tue, 17 December 2019 11:22 Go to previous messageGo to next message
nbehrnd is currently offline  nbehrnd
Messages: 127
Registered: June 2019
Senior Member
Hello Patrick,

I understand your aim is to bring line wise structures deposit in independent columns into a cell in common.

If so, 1) convert the structures you already have in the .dwar file as SMILES. You find this function along chemistry -> from chemical structure -> Add SMILES code, to be applied for each column of structures. 2) To concatenate the SMILES, reach for Data -> Add Calculate Values. In the new sub-menu, you define a string addition, of the SMILES, as shown below:

index.php?t=getfile&id=132&private=0

After confirmation by «ok», DataWarrior creates a new column with the result. You then 3) convert the concatenated SMILES string into a sketch with Chemistry -> Add Structures From Name. This equally creates a niew column, with both molecules represented in one cell:

index.php?t=getfile&id=133&private=0

Norwid
Re: Row wise chemical reaction [message #733 is a reply to message #724] Tue, 17 December 2019 23:16 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 514
Registered: June 2014
Senior Member
If I understand correctly, you don't only want to combine two molecules, you rather want to react them, which would require one more step on top of Norwid's suggestion. Without a few nasty hacks, this is not possible right now. It would need a new functionality, where you could selected one or multiple structure columns as starting materials and define a generic reaction with an equal number of generic reactants that defines how to construct the product.

This wouldn't be too complicated, but is still too much to be included in the upcoming update. Maybe after that...
Re: Row wise chemical reaction [message #754 is a reply to message #733] Mon, 13 January 2020 23:02 Go to previous messageGo to next message
P_Fitz
Messages: 14
Registered: November 2019
Junior Member
Yes that is correct, I do not just want to have them next to each other, I want to react them. Thanks for your reply and for supporting Data Warrior!
Re: Row wise chemical reaction [message #1612 is a reply to message #733] Fri, 20 May 2022 01:57 Go to previous messageGo to next message
P_Fitz
Messages: 14
Registered: November 2019
Junior Member
Just curious if this was ever implemented. Thanks for making Datawarrior freely available and supporting it!
Re: Row wise chemical reaction [message #1619 is a reply to message #1612] Thu, 02 June 2022 14:56 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 514
Registered: June 2014
Senior Member
I just have implemented the feature and deployed it in the development version, which you can download as replacement files for the 5.5.0 version. The links appear in the fineprint of the download page after checking 'read and understood'. Now, when opening the 'Merge Columns' dialog and selecting some structure columns you can also specify a generic reaction that defines how to react the selected compound with each other. An example is in the help text accessible from the dialog. Please let me know, whether this works for you...
Re: Row wise chemical reaction [message #1636 is a reply to message #1619] Thu, 16 June 2022 00:24 Go to previous messageGo to next message
P_Fitz
Messages: 14
Registered: November 2019
Junior Member
Hi Thomas,

Thanks so much for implementing this feature. Based on how the help screen looks (the suzuki reaction example) this is exactly how I want this feature to work. I've been trying to do the same thing with amide formation and it does not seem to be working. I went back and drew the same reaction scheme (at least I think so) for enumerating a library and that works. The numbering when I connected the bonds was slightly different there.

I'm not sure why, but after I draw the reaction, the A and B reactants seem to get switched. I think maybe the carboxylic acid is being interpreted as an fmoc amino acid and since it does not have an fmoc amino acid I'm getting an empty column as the reaction product. I've attached a screenshot of the reaction and my data columns. The output of the reaction is as I said an empty column.

As always, thanks for continuing to support Data warrior!

Patrick Fitzgerald
Re: Row wise chemical reaction [message #1637 is a reply to message #1636] Thu, 16 June 2022 00:27 Go to previous messageGo to next message
P_Fitz
Messages: 14
Registered: November 2019
Junior Member
I switched the order of my columns in the Table view and that seemed to work to do combine the molecules. This was reproducible. Switching them back stopped it from working, and then switching them again made it work.
Re: Row wise chemical reaction [message #1642 is a reply to message #1637] Mon, 20 June 2022 20:34 Go to previous messageGo to next message
nbehrnd is currently offline  nbehrnd
Messages: 127
Registered: June 2019
Senior Member
Dear Thomas,

For the nicely working «merge by reaction» function, I would like to file for feature suggestion. May one extend the reaction editor's functionality to match the one already present when running chemistry -> enumerate combinatorial library, i.e. to add

+ define .and. save (eventually re-use) a reaction with user defined name in the .rxn format
+ access the already available templates of the combinatorial library (Stille, Wittig, etc.)

By now, the GUI of the two seem to differ:

/forum/index.php?t=getfile&id=567&private=0

The observations refer to DW 5.5.0 for Linux including the update by 2022-06-17.

Norwid

[Updated on: Mon, 20 June 2022 20:36]

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Re: Row wise chemical reaction [message #1643 is a reply to message #1642] Mon, 20 June 2022 20:44 Go to previous messageGo to next message
nbehrnd is currently offline  nbehrnd
Messages: 127
Registered: June 2019
Senior Member
Dear Thomas,

related to the above feature suggest is a second one, this time to extend working via chemistry -> enumerate combinatorial library.

So far, reactants either are to be sketched again .or. load from a file about either one of the reactants. Would it be possible to extend the «add» function so that one may refer back to the currently open file to define the starting material by column? With the above test file reactions.dwar, this would be to point to column «amines» for one, and «chlorides» for the second line when «enumerate combinatorial library» asks for the reagents to permutate with each other.

/forum/index.php?t=getfile&id=569&private=0

At present «merge by reaction» constraints the set of products generated to reactions line-by-line.

Norwid
Re: Row wise chemical reaction [message #1648 is a reply to message #1636] Sat, 25 June 2022 15:48 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 514
Registered: June 2014
Senior Member
Hi Patrick,

yes, you are right. The reactants got switched, because they were encoded in lexical order by mistake, when they were stored as part of the task configuration. I have corrected this issue now in the current dev version.

Thank you for pointing me to the problem so clearly.

Thomas
Re: Row wise chemical reaction [message #1656 is a reply to message #1648] Tue, 28 June 2022 19:30 Go to previous message
P_Fitz
Messages: 14
Registered: November 2019
Junior Member
I'm glad my comment made sense! Thanks for being so receptive to feedback/changes.
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